Re the wife visiting i was more interested in knowing if she visits you after you are checked to line and flying and having your normal 9/10 days off will you have to leave the country then as a part of your contract or can you remain in Japan with her.
You can and people do it regularly to explore Japan while on their block of 10 days off. You do need to advice the girls in the office so that they arrange a shore pass with a transfer to your next duty flight because it does go beyond the standard 7 days of a shore pass. This is something that immigration does regularly with seamen that come to repair ships in the large shipping industry in Japan and go for extended period of time on their shore passes. Now there is a catch, the shore pass restricts you to the metropolitan area (or the area of the port where you entered Japan) and you are not supposed to venture beyond the area covered by the shore pass but guys go to give an example skiing in the mountains, scuba diving in Okinawa, or in my case I have gone to Nagoya to visit with friends. The only thing that is recommended is to take your company ID with you just in case you get stopped by the police on a regular check (they do this on occasion) if you produce your company ID, they will bow and go on their merry way.